data_1DQF # _entry.id 1DQF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1DQF pdb_00001dqf 10.2210/pdb1dqf/pdb NDB AR0026 ? ? RCSB RCSB010292 ? ? WWPDB D_1000010292 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2000-11-13 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-11-16 5 'Structure model' 1 4 2024-02-07 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_struct_conn_angle 5 5 'Structure model' struct_conn 6 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 18 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 19 5 'Structure model' '_pdbx_struct_conn_angle.value' 20 5 'Structure model' '_struct_conn.pdbx_dist_value' 21 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 22 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 23 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 24 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 25 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 26 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 27 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 28 5 'Structure model' '_struct_conn.ptnr1_symmetry' 29 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 30 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 31 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 32 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 33 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 34 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 35 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 36 5 'Structure model' '_struct_conn.ptnr2_symmetry' 37 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 38 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 39 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DQF _pdbx_database_status.recvd_initial_deposition_date 2000-01-04 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1DQH _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Xiong, Y.' 1 'Sundaralingam, M.' 2 # _citation.id primary _citation.title 'Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge.' _citation.journal_abbrev RNA _citation.journal_volume 6 _citation.page_first 1316 _citation.page_last 1324 _citation.year 2000 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10999608 _citation.pdbx_database_id_DOI 10.1017/S135583820000090X # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Xiong, Y.' 1 ? primary 'Sundaralingam, M.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)-3') ; 2806.735 1 ? ? 'HELIX II OF 5S RRNA' ? 2 polymer syn ;RNA (5'-R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3') ; 3231.988 1 ? ? ? ? 3 non-polymer syn 'CALCIUM ION' 40.078 2 ? ? ? ? 4 water nat water 18.015 38 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GCCACCCUG GCCACCCUG A ? 2 polyribonucleotide no no CAGGGUCGGC CAGGGUCGGC B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'CALCIUM ION' CA 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 C n 1 4 A n 1 5 C n 1 6 C n 1 7 C n 1 8 U n 1 9 G n 2 1 C n 2 2 A n 2 3 G n 2 4 G n 2 5 G n 2 6 U n 2 7 C n 2 8 G n 2 9 G n 2 10 C n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 C 2 2 2 C C A . n A 1 3 C 3 3 3 C C A . n A 1 4 A 4 4 4 A A A . n A 1 5 C 5 5 5 C C A . n A 1 6 C 6 6 6 C C A . n A 1 7 C 7 7 7 C C A . n A 1 8 U 8 8 8 U U A . n A 1 9 G 9 9 9 G G A . n B 2 1 C 1 10 10 C C B . n B 2 2 A 2 11 11 A A B . n B 2 3 G 3 12 12 G G B . n B 2 4 G 4 13 13 G G B . n B 2 5 G 5 14 14 G G B . n B 2 6 U 6 15 15 U U B . n B 2 7 C 7 16 16 C C B . n B 2 8 G 8 17 17 G G B . n B 2 9 G 9 18 18 G G B . n B 2 10 C 10 19 19 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 CA 1 201 201 CA CA B . D 3 CA 1 202 202 CA CA B . E 4 HOH 1 102 102 HOH WAT A . E 4 HOH 2 113 113 HOH WAT A . E 4 HOH 3 114 114 HOH WAT A . E 4 HOH 4 115 115 HOH WAT A . E 4 HOH 5 123 123 HOH WAT A . E 4 HOH 6 124 124 HOH WAT A . E 4 HOH 7 125 125 HOH WAT A . E 4 HOH 8 127 127 HOH WAT A . E 4 HOH 9 128 128 HOH WAT A . E 4 HOH 10 132 132 HOH WAT A . E 4 HOH 11 134 134 HOH WAT A . E 4 HOH 12 137 137 HOH WAT A . F 4 HOH 1 101 101 HOH WAT B . F 4 HOH 2 103 103 HOH WAT B . F 4 HOH 3 104 104 HOH WAT B . F 4 HOH 4 105 105 HOH WAT B . F 4 HOH 5 106 106 HOH WAT B . F 4 HOH 6 107 107 HOH WAT B . F 4 HOH 7 108 108 HOH WAT B . F 4 HOH 8 109 109 HOH WAT B . F 4 HOH 9 110 110 HOH WAT B . F 4 HOH 10 111 111 HOH WAT B . F 4 HOH 11 112 112 HOH WAT B . F 4 HOH 12 116 116 HOH WAT B . F 4 HOH 13 117 117 HOH WAT B . F 4 HOH 14 118 118 HOH WAT B . F 4 HOH 15 119 119 HOH WAT B . F 4 HOH 16 120 120 HOH WAT B . F 4 HOH 17 121 121 HOH WAT B . F 4 HOH 18 122 122 HOH WAT B . F 4 HOH 19 126 126 HOH WAT B . F 4 HOH 20 129 129 HOH WAT B . F 4 HOH 21 130 130 HOH WAT B . F 4 HOH 22 131 131 HOH WAT B . F 4 HOH 23 133 133 HOH WAT B . F 4 HOH 24 135 135 HOH WAT B . F 4 HOH 25 136 136 HOH WAT B . F 4 HOH 26 138 138 HOH WAT B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal AMoRE phasing . ? 1 CNS refinement 0.9 ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _cell.entry_id 1DQF _cell.length_a 57.15 _cell.length_b 57.15 _cell.length_c 43.54 _cell.angle_alpha 90.0 _cell.angle_beta 90.0 _cell.angle_gamma 90.0 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 1DQF _symmetry.space_group_name_H-M 'P 42 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting tetragonal _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1DQF _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 58.21 _exptl_crystal.density_Matthews 2.94 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details 'MGCL2, CACL2, CACODYLATE, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MGCL2 ? ? ? 1 2 1 CACL2 ? ? ? 1 3 1 CACODYLATE ? ? ? 1 4 1 MPD ? ? ? 1 5 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 263 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU300' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1DQF _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 25.57 _reflns.d_resolution_high 2.2 _reflns.number_obs 3757 _reflns.number_all 3962 _reflns.percent_possible_obs 94.8 _reflns.pdbx_Rmerge_I_obs 0.0770000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 14 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.6 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1DQF _refine.ls_number_reflns_obs 3757 _refine.ls_number_reflns_all 3962 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.0 _refine.ls_d_res_high 2.2 _refine.ls_percent_reflns_obs 94.9 _refine.ls_R_factor_obs 0.2040000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2040000 _refine.ls_R_factor_R_free 0.2210000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 8.5 _refine.ls_number_reflns_R_free 404 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values CNS _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_phase_error ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 399 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 439 _refine_hist.d_res_high 2.2 _refine_hist.d_res_low 10.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.26 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1DQF _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1DQF _struct.title 'CRYSTAL STRUCTURE OF HELIX II OF THE X. LAEVIS SOMATIC 5S RRNA WITH A CYTOSINE BULGE IN TWO CONFORMATIONS' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DQF _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'DOUBLE HELIX, CYTOSINE BULGE, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 4 ? F N N 4 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 1 PDB 1DQF 1DQF ? ? ? 2 2 PDB 1DQF 1DQF ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1DQF A 1 ? 9 ? 1DQF 1 ? 9 ? 1 9 2 2 1DQF B 1 ? 10 ? 1DQF 10 ? 19 ? 10 19 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A U 8 OP1 ? ? ? 5_645 C CA . CA ? ? A U 8 B CA 201 1_555 ? ? ? ? ? ? ? 2.437 ? ? metalc2 metalc ? ? A G 9 OP1 ? ? ? 5_645 D CA . CA ? ? A G 9 B CA 202 1_555 ? ? ? ? ? ? ? 2.166 ? ? metalc3 metalc ? ? A G 9 OP1 ? ? ? 3_645 D CA . CA ? ? A G 9 B CA 202 1_555 ? ? ? ? ? ? ? 2.166 ? ? metalc4 metalc ? ? B C 10 "O3'" ? ? ? 1_555 C CA . CA ? ? B C 19 B CA 201 1_555 ? ? ? ? ? ? ? 2.361 ? ? metalc5 metalc ? ? B C 10 "O2'" ? ? ? 1_555 C CA . CA ? ? B C 19 B CA 201 1_555 ? ? ? ? ? ? ? 2.643 ? ? metalc6 metalc ? ? B C 10 OP1 ? ? ? 1_555 D CA . CA ? ? B C 19 B CA 202 1_555 ? ? ? ? ? ? ? 2.253 ? ? metalc7 metalc ? ? B C 10 OP1 ? ? ? 8_666 D CA . CA ? ? B C 19 B CA 202 1_555 ? ? ? ? ? ? ? 2.253 ? ? metalc8 metalc ? ? F HOH . O ? ? ? 1_555 C CA . CA ? ? B HOH 101 B CA 201 1_555 ? ? ? ? ? ? ? 2.493 ? ? metalc9 metalc ? ? F HOH . O ? ? ? 1_555 C CA . CA ? ? B HOH 105 B CA 201 1_555 ? ? ? ? ? ? ? 2.217 ? ? metalc10 metalc ? ? F HOH . O ? ? ? 1_555 C CA . CA ? ? B HOH 106 B CA 201 1_555 ? ? ? ? ? ? ? 2.323 ? ? metalc11 metalc ? ? F HOH . O ? ? ? 1_555 D CA . CA ? ? B HOH 107 B CA 202 1_555 ? ? ? ? ? ? ? 2.287 ? ? metalc12 metalc ? ? F HOH . O ? ? ? 8_666 D CA . CA ? ? B HOH 107 B CA 202 1_555 ? ? ? ? ? ? ? 2.287 ? ? metalc13 metalc ? ? F HOH . O ? ? ? 1_555 C CA . CA ? ? B HOH 120 B CA 201 1_555 ? ? ? ? ? ? ? 2.304 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 1 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 1 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 1 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 2 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 2 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 2 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 3 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 3 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 3 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 4 B U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 4 B U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 5 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 5 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 5 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 6 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 6 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 6 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 2 N1 ? ? A U 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 8 O4 ? ? ? 1_555 B A 2 N6 ? ? A U 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 9 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 9 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 9 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B C 7 N4 ? ? ? 1_555 B G 9 O6 ? ? B C 16 B G 18 7_556 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog27 hydrog ? ? B G 9 O6 ? ? ? 1_555 B C 7 N4 ? ? B G 18 B C 16 7_556 ? ? ? ? ? ? 'G-C PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP1 ? A U 8 ? A U 8 ? 5_645 CA ? C CA . ? B CA 201 ? 1_555 "O3'" ? B C 10 ? B C 19 ? 1_555 100.6 ? 2 OP1 ? A U 8 ? A U 8 ? 5_645 CA ? C CA . ? B CA 201 ? 1_555 "O2'" ? B C 10 ? B C 19 ? 1_555 83.6 ? 3 "O3'" ? B C 10 ? B C 19 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 "O2'" ? B C 10 ? B C 19 ? 1_555 72.1 ? 4 OP1 ? A U 8 ? A U 8 ? 5_645 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 101 ? 1_555 91.6 ? 5 "O3'" ? B C 10 ? B C 19 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 101 ? 1_555 74.9 ? 6 "O2'" ? B C 10 ? B C 19 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 101 ? 1_555 145.1 ? 7 OP1 ? A U 8 ? A U 8 ? 5_645 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 105 ? 1_555 164.2 ? 8 "O3'" ? B C 10 ? B C 19 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 105 ? 1_555 89.7 ? 9 "O2'" ? B C 10 ? B C 19 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 105 ? 1_555 88.3 ? 10 O ? F HOH . ? B HOH 101 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 105 ? 1_555 102.8 ? 11 OP1 ? A U 8 ? A U 8 ? 5_645 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 106 ? 1_555 82.3 ? 12 "O3'" ? B C 10 ? B C 19 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 106 ? 1_555 143.2 ? 13 "O2'" ? B C 10 ? B C 19 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 106 ? 1_555 71.8 ? 14 O ? F HOH . ? B HOH 101 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 106 ? 1_555 141.9 ? 15 O ? F HOH . ? B HOH 105 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 106 ? 1_555 82.2 ? 16 OP1 ? A U 8 ? A U 8 ? 5_645 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 120 ? 1_555 101.1 ? 17 "O3'" ? B C 10 ? B C 19 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 120 ? 1_555 142.2 ? 18 "O2'" ? B C 10 ? B C 19 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 120 ? 1_555 141.0 ? 19 O ? F HOH . ? B HOH 101 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 120 ? 1_555 73.9 ? 20 O ? F HOH . ? B HOH 105 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 120 ? 1_555 76.9 ? 21 O ? F HOH . ? B HOH 106 ? 1_555 CA ? C CA . ? B CA 201 ? 1_555 O ? F HOH . ? B HOH 120 ? 1_555 70.5 ? 22 OP1 ? A G 9 ? A G 9 ? 5_645 CA ? D CA . ? B CA 202 ? 1_555 OP1 ? A G 9 ? A G 9 ? 3_645 102.9 ? 23 OP1 ? A G 9 ? A G 9 ? 5_645 CA ? D CA . ? B CA 202 ? 1_555 OP1 ? B C 10 ? B C 19 ? 1_555 90.3 ? 24 OP1 ? A G 9 ? A G 9 ? 3_645 CA ? D CA . ? B CA 202 ? 1_555 OP1 ? B C 10 ? B C 19 ? 1_555 98.2 ? 25 OP1 ? A G 9 ? A G 9 ? 5_645 CA ? D CA . ? B CA 202 ? 1_555 OP1 ? B C 10 ? B C 19 ? 8_666 98.2 ? 26 OP1 ? A G 9 ? A G 9 ? 3_645 CA ? D CA . ? B CA 202 ? 1_555 OP1 ? B C 10 ? B C 19 ? 8_666 90.3 ? 27 OP1 ? B C 10 ? B C 19 ? 1_555 CA ? D CA . ? B CA 202 ? 1_555 OP1 ? B C 10 ? B C 19 ? 8_666 166.4 ? 28 OP1 ? A G 9 ? A G 9 ? 5_645 CA ? D CA . ? B CA 202 ? 1_555 O ? F HOH . ? B HOH 107 ? 1_555 168.2 ? 29 OP1 ? A G 9 ? A G 9 ? 3_645 CA ? D CA . ? B CA 202 ? 1_555 O ? F HOH . ? B HOH 107 ? 1_555 88.0 ? 30 OP1 ? B C 10 ? B C 19 ? 1_555 CA ? D CA . ? B CA 202 ? 1_555 O ? F HOH . ? B HOH 107 ? 1_555 83.6 ? 31 OP1 ? B C 10 ? B C 19 ? 8_666 CA ? D CA . ? B CA 202 ? 1_555 O ? F HOH . ? B HOH 107 ? 1_555 86.1 ? 32 OP1 ? A G 9 ? A G 9 ? 5_645 CA ? D CA . ? B CA 202 ? 1_555 O ? F HOH . ? B HOH 107 ? 8_666 88.0 ? 33 OP1 ? A G 9 ? A G 9 ? 3_645 CA ? D CA . ? B CA 202 ? 1_555 O ? F HOH . ? B HOH 107 ? 8_666 168.2 ? 34 OP1 ? B C 10 ? B C 19 ? 1_555 CA ? D CA . ? B CA 202 ? 1_555 O ? F HOH . ? B HOH 107 ? 8_666 86.1 ? 35 OP1 ? B C 10 ? B C 19 ? 8_666 CA ? D CA . ? B CA 202 ? 1_555 O ? F HOH . ? B HOH 107 ? 8_666 83.6 ? 36 O ? F HOH . ? B HOH 107 ? 1_555 CA ? D CA . ? B CA 202 ? 1_555 O ? F HOH . ? B HOH 107 ? 8_666 81.6 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B CA 201 ? 6 'BINDING SITE FOR RESIDUE CA B 201' AC2 Software B CA 202 ? 6 'BINDING SITE FOR RESIDUE CA B 202' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 U A 8 ? U A 8 . ? 5_645 ? 2 AC1 6 C B 10 ? C B 19 . ? 1_555 ? 3 AC1 6 HOH F . ? HOH B 101 . ? 1_555 ? 4 AC1 6 HOH F . ? HOH B 105 . ? 1_555 ? 5 AC1 6 HOH F . ? HOH B 106 . ? 1_555 ? 6 AC1 6 HOH F . ? HOH B 120 . ? 1_555 ? 7 AC2 6 G A 9 ? G A 9 . ? 5_645 ? 8 AC2 6 G A 9 ? G A 9 . ? 3_645 ? 9 AC2 6 C B 10 ? C B 19 . ? 8_666 ? 10 AC2 6 C B 10 ? C B 19 . ? 1_555 ? 11 AC2 6 HOH F . ? HOH B 107 . ? 1_555 ? 12 AC2 6 HOH F . ? HOH B 107 . ? 8_666 ? # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id G _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 14 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.073 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 B CA 202 ? D CA . 2 1 B HOH 122 ? F HOH . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 CA CA CA N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 HOH O O N N 112 HOH H1 H N N 113 HOH H2 H N N 114 U OP3 O N N 115 U P P N N 116 U OP1 O N N 117 U OP2 O N N 118 U "O5'" O N N 119 U "C5'" C N N 120 U "C4'" C N R 121 U "O4'" O N N 122 U "C3'" C N S 123 U "O3'" O N N 124 U "C2'" C N R 125 U "O2'" O N N 126 U "C1'" C N R 127 U N1 N N N 128 U C2 C N N 129 U O2 O N N 130 U N3 N N N 131 U C4 C N N 132 U O4 O N N 133 U C5 C N N 134 U C6 C N N 135 U HOP3 H N N 136 U HOP2 H N N 137 U "H5'" H N N 138 U "H5''" H N N 139 U "H4'" H N N 140 U "H3'" H N N 141 U "HO3'" H N N 142 U "H2'" H N N 143 U "HO2'" H N N 144 U "H1'" H N N 145 U H3 H N N 146 U H5 H N N 147 U H6 H N N 148 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1DQF 'double helix' 1DQF 'a-form double helix' 1DQF 'bulge loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B C 10 1_555 -0.448 -0.147 0.549 11.945 -12.477 1.508 1 A_G1:C19_B A 1 ? B 19 ? 19 1 1 A C 2 1_555 B G 9 1_555 0.362 -0.150 0.018 10.886 -13.820 1.853 2 A_C2:G18_B A 2 ? B 18 ? 19 1 1 A C 3 1_555 B G 8 1_555 0.248 -0.401 -0.144 6.954 -10.273 -0.708 3 A_C3:G17_B A 3 ? B 17 ? 19 1 1 A A 4 1_555 B U 6 1_555 0.363 -0.402 0.191 7.747 -9.525 -2.155 4 A_A4:U15_B A 4 ? B 15 ? 20 1 1 A C 5 1_555 B G 5 1_555 0.657 -0.634 -0.031 12.344 -14.323 -1.511 5 A_C5:G14_B A 5 ? B 14 ? 19 1 1 A C 6 1_555 B G 4 1_555 0.117 -0.447 -0.088 4.483 -11.154 2.366 6 A_C6:G13_B A 6 ? B 13 ? 19 1 1 A C 7 1_555 B G 3 1_555 0.247 -0.290 -0.141 3.139 -8.227 0.187 7 A_C7:G12_B A 7 ? B 12 ? 19 1 1 A U 8 1_555 B A 2 1_555 -0.149 -0.385 -0.086 0.373 -12.010 2.182 8 A_U8:A11_B A 8 ? B 11 ? 20 1 1 A G 9 1_555 B C 1 1_555 -0.569 -0.002 0.042 -7.880 -13.675 6.108 9 A_G9:C10_B A 9 ? B 10 ? 19 1 1 B C 7 1_555 B G 9 7_556 0.163 3.099 0.198 -2.556 -3.697 64.865 10 B_C16:G18_B B 16 ? B 18 ? ? ? 1 B C 7 1_555 B G 9 1_555 0.163 3.099 0.198 -2.556 -3.697 64.865 11 B_C16:G18_B B 16 ? B 18 ? ? ? # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 10 1_555 A C 2 1_555 B G 9 1_555 -0.863 -1.410 3.359 0.306 2.751 35.463 -2.713 1.457 3.236 4.508 -0.501 35.568 1 AA_G1C2:G18C19_BB A 1 ? B 19 ? A 2 ? B 18 ? 1 A C 2 1_555 B G 9 1_555 A C 3 1_555 B G 8 1_555 0.340 -2.130 3.254 -0.404 8.196 31.661 -5.083 -0.668 2.631 14.715 0.726 32.681 2 AA_C2C3:G17G18_BB A 2 ? B 18 ? A 3 ? B 17 ? 1 A C 3 1_555 B G 8 1_555 A A 4 1_555 B U 6 1_555 0.385 -1.722 3.270 -4.745 6.128 38.179 -3.292 -1.126 2.903 9.252 7.164 38.929 3 AA_C3A4:U15G17_BB A 3 ? B 17 ? A 4 ? B 15 ? 1 A A 4 1_555 B U 6 1_555 A C 5 1_555 B G 5 1_555 0.100 -1.153 3.185 0.914 5.513 37.920 -2.412 -0.044 2.996 8.428 -1.397 38.314 4 AA_A4C5:G14U15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A C 5 1_555 B G 5 1_555 A C 6 1_555 B G 4 1_555 -0.296 -1.815 3.516 -0.284 5.190 27.818 -4.947 0.539 3.135 10.676 0.585 28.290 5 AA_C5C6:G13G14_BB A 5 ? B 14 ? A 6 ? B 13 ? 1 A C 6 1_555 B G 4 1_555 A C 7 1_555 B G 3 1_555 -0.276 -1.805 3.361 -0.969 7.981 31.394 -4.591 0.331 2.836 14.454 1.755 32.382 6 AA_C6C7:G12G13_BB A 6 ? B 13 ? A 7 ? B 12 ? 1 A C 7 1_555 B G 3 1_555 A U 8 1_555 B A 2 1_555 0.518 -1.569 3.287 0.915 7.224 31.170 -4.094 -0.782 2.874 13.219 -1.675 31.988 7 AA_C7U8:A11G12_BB A 7 ? B 12 ? A 8 ? B 11 ? 1 A U 8 1_555 B A 2 1_555 A G 9 1_555 B C 1 1_555 0.329 -1.696 3.552 2.065 7.953 29.164 -4.891 -0.203 3.010 15.413 -4.001 30.275 8 AA_U8G9:C10A11_BB A 8 ? B 11 ? A 9 ? B 10 ? # _atom_sites.entry_id 1DQF _atom_sites.fract_transf_matrix[1][1] 0.017498 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.017498 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.022967 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CA N O P # loop_